Cobalt in PDB 3gqa: Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in Complex with Cobalt Ions

The structure of Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in Complex with Cobalt Ions, PDB code: 3gqa was solved by Y.Xiang, M.G.Rossmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.88 / 2.10
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	89.741, 89.741, 584.795, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 22.2

The binding sites of Cobalt atom in the Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in Complex with Cobalt Ions (pdb code 3gqa). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in Complex with Cobalt Ions, PDB code: 3gqa:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in Complex with Cobalt Ions


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in Complex with Cobalt Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1 b:34.2 occ:1.00 OD2 A:ASP312 1.9 26.7 1.0 O A:HOH813 2.0 24.4 1.0 NE2 A:HIS285 2.1 24.8 1.0 O A:HOH811 2.1 41.0 1.0 O A:HOH814 2.7 40.7 1.0 CG A:ASP312 3.0 27.1 1.0 CE1 A:HIS285 3.1 21.6 1.0 CD2 A:HIS285 3.1 23.3 1.0 OE1 A:GLU310 3.2 32.9 1.0 CB A:ASP312 3.5 24.1 1.0 OD1 A:ASP312 4.1 29.6 1.0 O A:HOH812 4.2 40.1 1.0 ND1 A:HIS285 4.2 23.1 1.0 OG1 A:THR283 4.2 23.8 1.0 NE2 A:HIS337 4.2 41.6 1.0 CG A:HIS285 4.3 23.9 1.0 CD A:GLU310 4.3 27.1 1.0 OD2 A:ASP280 4.5 27.4 1.0 NE2 A:HIS240 4.8 25.3 1.0 CE1 A:HIS240 4.8 27.1 1.0 CD2 A:HIS337 4.8 39.3 1.0 CZ A:TYR251 4.9 32.0 1.0 CG A:GLU310 4.9 25.1 1.0 OD1 A:ASP279 4.9 31.3 1.0 OD2 A:ASP313 5.0 30.2 1.0 CE1 A:TYR251 5.0 31.3 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in Complex with Cobalt Ions


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in Complex with Cobalt Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Co2 b:36.4 occ:1.00 O A:HOH812 2.0 40.1 1.0 OD2 A:ASP280 2.1 27.4 1.0 OE2 A:GLU310 2.1 27.5 1.0 OD2 A:ASP279 2.2 31.6 1.0 OD1 A:ASP280 2.2 28.8 1.0 CG A:ASP280 2.5 28.3 1.0 O A:ASN305 2.5 32.9 1.0 CD A:GLU310 3.1 27.1 1.0 CG A:ASP279 3.1 30.0 1.0 OE1 A:GLU310 3.4 32.9 1.0 OD1 A:ASP279 3.4 31.3 1.0 ND2 A:ASN305 3.6 35.2 1.0 C A:ASN305 3.7 32.9 1.0 ND2 A:ASN307 3.8 24.0 1.0 CB A:ASP280 4.0 26.8 1.0 CG A:ASN305 4.2 35.5 1.0 C A:ASP279 4.3 28.5 1.0 O A:HOH813 4.3 24.4 1.0 O A:HOH811 4.3 41.0 1.0 CG A:GLU310 4.3 25.1 1.0 CB A:ASP279 4.4 29.5 1.0 CB A:ASN305 4.4 34.0 1.0 N A:ASN307 4.4 28.0 1.0 N A:ASP280 4.4 27.3 1.0 O A:ASP279 4.5 27.9 1.0 CG A:ASN307 4.5 27.3 1.0 CA A:CYS306 4.6 30.3 1.0 CB A:GLU310 4.6 24.4 1.0 N A:CYS306 4.6 31.3 1.0 CA A:ASP280 4.6 26.8 1.0 CA A:ASN305 4.7 33.9 1.0 CA A:ASP279 4.7 28.9 1.0 CB A:ASN307 4.7 27.3 1.0 OD1 A:ASN305 5.0 36.3 1.0

Y.Xiang, P.G.Leiman, L.Li, S.Grimes, D.L.Anderson, M.G.Rossmann. Crystallographic Insights Into the Autocatalytic Assembly Mechanism of A Bacteriophage Tail Spike. Mol.Cell V. 34 375 2009.
ISSN: ISSN 1097-2765
PubMed: 19450535
DOI: 10.1016/J.MOLCEL.2009.04.009